Version release associated with GitHub repository: https://github.com/leahcrowe-otago/FBD_measurements/tree/main

1. Identify when in video dolphin surfaces, ID that dolphin
2. Screen grab the best image of the dolphin above that shows rostrum to tail at/near the surface

• used VLC player to go frame by frame

1. Add screen grab filename to the time and ID from #1
2. Run "./scripts/Altitudes for snapshots" for each day of droning

• this adds a check to make sure GPS of the LiDAR and the metadata from the drone match up
• finds altitude for each snapshot
• matches up to IDs and outputs file to enter measurements
• identifies if altimeter reading meets criteria per Dickson et al. 2020 ("issues" column)

1. Populate the "altperimage_*" file with measurements (.csvs from Whalelength are later merged in "./scripts/whalength_file_merge.R")

• filter by issue == "N"
• hide columns C, G, H, and J to AC
• Run each resulting image through Whalength
  • I1P Video stills, -1.5 cm offset

1. Run "measurements_demo.Rmd" to wrangle data, incorporate life history info ("demo"graphy data), and create some supplementary figures

• calls "whalength_file_merge.R"
  • merges all Whalelength outputs
  • creates Fig. S4, calibration measurements
• Supplementary Figures S5
• data output: see data repo for metadata details
  • individual i measurement data at each capture occasion j for model
  • individual life history data

1. Model run in the "./scripts/stan/runstan_allo_mv_t0.R" file: 'run' the 'stan' code of 'allo'metric measurement data in a 'm'ulti'v'ariate model with fixed age at length zero (t0)

• data formatting for model
• calls the Stan model
  • main model: "./scripts/stan/vb_mod_all0_t0.stan"
  • for the supplementary sex/pod effect model: "./scripts/stan/sex_pod_effects.R" runs the model specified in "./scripts/stan/vb_mod_all0_t0_sexpod.stan"
• initial values for von Bertalanffy model (init_vb)
• fit the model (fit_vb)
• save results

1. "./scripts/Results.R"

• read data
• summarise results
• create table S2
• create Figs. 2–4, S6, S7

1. "Supplementary.qmd" creates the suppmat file

• creates supplementary tables
• Section 1.3 created from './scripts/Results_age_adjusted.R'
• Fig. S1 map created by calling "./scripts/ms_map.R"

1. Data: "./data/Measurements/Data for review"

• Metadata-description.pdf: describes the data in the following files:
  • ij_1.csv
  • ij_2.csv
  • ij_3.csv
  • ij_ID.csv